Check that the front axle is all the way in. If you don't follow the right sequence in putting the front wheel back on and the axle is not seated all the way in, the caliper mounting bracket will rub against the brake disk mounting bolts.
The left side of the axle should be flush with the fork, no part of it sticking out. If that is what it is, then make sure the left side pinch bolts are loose and just lightly pull on the left side fork. You will hear a "toink" sound and the fork should slide over about a 1/4".
Before you tighten the pinch bolts. Take the bike off the lift and sit on it. Push up and down on the handlebars to compress the front suspension, this will seat everything properly. Then tighten the pinch bolts up to spec.
This is a common issue if you don't have the axle seated and don't follow the proper tightening sequence.
At the bottom of this thread is a picture of the improper, then proper photo of the how the axle should look:
http://www.valkyrieforum.com/bbs/index.php/topic,26572.msg241288.html#msg241288